Fabian Egli

@sralchemab Good to know. Thank you for reporting this use case. It would be great to have a test case for a regression test in any case. [Edited to remove...

Is it not unexpected Nextflow behaviour that a setting specifically for conda can impact a run with docker?

The only thing changing between the CI run that is failing and the one that is not is the following line in the [preprocess_expdesign.nf](https://github.com/nf-core/quantms/pull/53/commits/37ab2effcec88ce55e9cb72f6f10d30d76effb9d#diff-250becd2f41b02582ba265325f3ed59d1e54c99726f56d2fce7b4d170ab8c250) file: ``` conda (params.enable_conda ? "bioconda::sdrf-pipelines=0.0.21"...

Here are the links to the failed test https://github.com/nf-core/quantms/runs/8189234530?check_suite_focus=true and the one that succeeds https://github.com/nf-core/quantms/runs/8190591520?check_suite_focus=true

> [...] not even understand what is failing We have that in common. And I hoped someone here might be able to figure it out. Interestingly it is working with...

BTW: The conda ennvironment seems to be not activated in some cases, see [this test](https://github.com/nf-core/quantms/runs/8305326957?check_suite_focus=true) where I expose the conda environment variable `CONDA_DEFAULT_ENV` which should probably be 'base' but is...

@jasongrout Thank you, that works. I wonder if this could be a checkbox somewhere in the settings for users on macOS?

Bioconda also uses channel priority `strict`. Should we test for that, too?

I am not familiar with the use of C++ extensions and don't know either. Could you try and find out if it works with an explicit import? e.g. try adding...

I don't quite follow why this is not scalable - or why this would matter much here. I would not start ignoring things - the linting to date isn't (expected...